Kolmogorov Complexity With DNA Data in Python
Analyzing the complexity of DNA sequences using Kolmogorov Complexity is not difficult. However, it requires some background which I will present in this thorough tutorial 😊!
Table of Contents
Introduction: 00:00
What is a DNA Sequence?: 03:35
Kolmogorov Complexity: 06:20
Paper Walkthrough: 09:31
Lempel-Ziv Complexity: 14:03
Data Pipeline Overview: 17:20
Code Walkthrough: 20:44
Spatial Complexity Graph: 31:04
Read the paper yo: 34:11
Conclusion: 35:15
✍️ Blog post for this video can be found here: https://www.yacinemahdid.com/kolmogor...
Kolmogorov Complexity
In a nutshell, the kolmogorov (K) complexity is simply the size of the shortest program that can produce the desired object.It can be approximated by Lempel-Ziv complexity!
Lempel-Ziv
Lempel-Ziv complexity stems directly from the LZ type of lossless compression algorithm, where the two popular ones are LZ77 and LZ78.
Basically, to get LZ complexity you just need to take these algorithms and pop-off the saving of the compressed information (i.e. which in practice is a bit overkill since even with the compression information we get a good upper-bound on the K complexity).
LZ77 youtube video recommendations: • Elegant Compression in Text (The LZ 7...
Credit
I've used this beautiful video of the DNA modelization: • DNA animation (2002-2014) by Drew Ber...
It's from WEHImovies, check out there stuff!
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